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SNPdetector specifications

Information


Unique identifier OMICS_14879
Name SNPdetector
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Perl
Computer skills Advanced
Stability No
Maintained No

Versioning


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Maintainer


This tool is not available anymore.

Publication for SNPdetector

SNPdetector citations

 (7)
library_books

The landscape of somatic mutations in Infant MLL rearranged acute lymphoblastic leukemias

2015
Nat Genet
PMCID: 4553269
PMID: 25730765
DOI: 10.1038/ng.3230

[…] genes were sequenced by Sanger sequencing (ABL1, AKT3, ALK, FOXO1, FOXO3, FOXO4, FOXO6, INPP5D, JAK2, MET, PDGFRA, PDGFRB, PTEN, RAF1, RET, SYK) and putative SNVs and indel variants were detected by SNPdetector. Non-silent sequence mutations were selected for validation by Sanger sequencing of both the tumor and matching normal samples (where available). […]

library_books

The genomic landscape of diffuse intrinsic pontine glioma and pediatric non brainstem high grade glioma

2014
Nat Genet
PMCID: 4056452
PMID: 24705251
DOI: 10.1038/ng.2938

[…] 1295347) was amplified by PCR from tumors and matched normal and sequenced by Sanger Sequencing using primers in to check for two previously described TERT promoter SNVs. Sequence was analyzed using SNPDetector and manual review was performed using Consed. […]

library_books

Whole genome sequencing identifies genetic alterations in pediatric low grade gliomas

2013
Nat Genet
PMCID: 3727232
PMID: 23583981
DOI: 10.1038/ng.2611

[…] s (e.g. FGFR2), and TP53.The analysis was undertaken using PCR-based 3730 capillary sequencing at Beckman Coulter Genomics, as previously described . Putative SNVs and indel variants were detected by SNPdetector25 . Non-silent coding variations present in tumor, but absent in normal tissue, were considered somatic mutations after manual review using the program consed. To remove additional germlin […]

library_books

Contrasting population genetic patterns within the white throated sparrow genome (Zonotrichia albicollis)

2010
BMC Genet
PMCID: 3223602
PMID: 21029465
DOI: 10.1186/1471-2156-11-96

[…] Nucleotide polymorphisms were automatically called using SNPdetector [] and manually confirmed prior to further analyses. Annotation of the gene features for each locus was based on the annotation of orthologous zebra finch genomic segments (taeGut1) []. In […]

library_books

A Genome Wide Survey of SNP Variation Reveals the Genetic Structure of Sheep Breeds

2009
PLoS One
PMCID: 2652362
PMID: 19270757
DOI: 10.1371/journal.pone.0004668

[…] X 384 liquid handler was used for large volume manipulations (4–20ul) and Deerac Equator GX-8 liquid handler was used for small volume manipulations (0.5–2ul). Polymorphic bases were identified using SNPdetector and polyphred v 5.01 . The 6021 SNP reported represent all of the nucleotide positions independently identified as polymorphic using both prediction programs. […]

library_books

A novel approach to sequence validating protein expression clones with automated decision making

2007
BMC Bioinformatics
PMCID: 1914086
PMID: 17567908
DOI: 10.1186/1471-2105-8-198

[…] -sequencing" projects (such as sequencing the same gene in many individuals to find polymorphisms) bear some similarity to the concept of clone validation (e.g., PolyBayes [], PolyPhred [], noSnp [], SNPdetector []). However none of these programs consider polypeptide consequences of differences nor do they provide a mechanism for applying acceptance criteria within the workflow. Moreover, SNP dis […]

Citations

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SNPdetector institution(s)
Laboratory of Population Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
SNPdetector funding source(s)
Supported by the Intramural Research Program of the Center for Cancer Research, NCI, National Institutes of Health.

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